Water samples were collected in Middle Amazonia from the Amazon River, Rio Negro and 17 tributaries of Rio Negro. The analyses consisted of pH, conductivity, and dissolved organic (DOC) measurements, as well as plasma source mass spectrometry (ICP-MS). Factor analysis revealed three factors, which explained 94% of the total variance. A plot of factor scores presented a cluster containing mostly samples from the Rio Negro Basin. Ultrafiltration tests confirmed that organics from the Rio Negro have higher molecular mass than in the Amazon, and that some metals are associated with these compounds. Heavy rare-earth elements (REE) are enriched relative to light REE in the dissolved fraction of most rivers of the Negro Basin; the opposite occurred in suspended matter.